In this study we report about the inner and outer structure of CuInS2 microspheres which might be used e.g. in pastes for simple, low-cost solar cell preparation, as well as in electrodes for light-driven water splitting. The microspheres are synthesized via a mild, template-free solvothermal synthesis route and characterised by electron and focused ion beam microscopy, X-ray diffraction, inductively coupled plasma atomic emission and energy dispersive X-ray spectroscopy. The investigations of cross sections prepared by focused ion beam showed that the spheres consist of compact cores and flaky surface structures. Depending on the reaction time, the core possesses a stoichiometric or Cu-rich chemical composition surrounded by an In-rich shell. The flaky surface always comprises a stoichiometric composition in tetragonal chalcopyrite crystal structure, whereas the other areas additionally show minor contributions of CuS, and CuInS2 in hexagonal wurtzite structure. The presence of different phases can be beneficial for future applications since they offer different absorption behaviour in the visible range.